AN EFFICIENT AND RAPID PROTOCOL FOR PLANT NUCLEAR DNA PREPARATION SUITABLE FOR NEXT GENERATION SEQUENCING METHODS

被引：18

作者：

Carrier, Gregory ^{[1
]}

Santoni, Sylvain ^{[2
]}

Rodier-Goud, Marguerite ^{[3
]}

Canaguier, Aurelie ^{[4
]}

de Kochko, Alexandre ^{[2
]}

Dubreuil-Tranchant, Christine ^{[2
]}

This, Patrice ^{[2
]}

Boursiquot, Jean-Michel ^{[2
]}

Le Cunff, Loic ^{[1
]}

机构：

[1] UMT Geno Vigne, IFV INRA Montpellier Supagro, F-34060 Montpellier, France

[2] INRA IRD Montpellier Supagro, UMR DIAPC 1097, F-34060 Montpellier, France

[3] Univ Montpellier 2, INRA, CIRAD, UMR DAP 1098, F-34398 Montpellier, France

[4] INRA CNRS Univ Evry Genom Vegetale, F-91057 Evry, France

来源：

AMERICAN JOURNAL OF BOTANY | 2011年 / 98卷 / 01期

关键词：

next generation sequencers; nuclear plant DNA extraction; nuclei isolation; GENOME; L;

D O I：

10.3732/ajb.1000371

中图分类号：

Q94 [植物学];

学科分类号：

071001 [植物学];

摘要：

Premise of the study : In this study, we developed a nuclear DNA extraction protocol for Next Generation Sequencers (NGS). Methods and Results : We applied this extraction method to grapevines and coffee trees, which are known to contain many secondary metabolites. The nuclear DNA obtained was sequenced by the 454/GS-FLX method. We obtained excellent results, with less than 4% cytoplasmic DNA, in a similar way to a BAC (Bacterial Artificial Chromosome)-building protocol. We also compared our protocol with a classic DNA extraction using specific cytoplasmic DNA amplification. Results showed a lower cytoplasmic DNA contamination with the new protocol. Conclusions : The method presented here is fast and economical. The DNA obtained is of high quality, with a low level of cytoplasmic DNA contamination, and very efficient for the construction of sequencing libraries.

引用

页码：E13 / E15

页数：3

共 10 条

[1]

CHLOROPLAST DNA LEVELS AND THE CONTROL OF CHLOROPLAST DIVISION IN LIGHT-GROWN WHEAT LEAVES [J].

BOFFEY, SA ;

LEECH, RM .

PLANT PHYSIOLOGY, 1982, 69 (06) :1387-1391

[2]

RAPID AND SIMPLE METHOD FOR PURIFICATION OF NUCLEIC-ACIDS [J].

BOOM, R ;

SOL, CJA ;

SALIMANS, MMM ;

JANSEN, CL ;

WERTHEIMVANDILLEN, PME ;

VANDERNOORDAA, J .

JOURNAL OF CLINICAL MICROBIOLOGY, 1990, 28 (03) :495-503

[3]

A database of PCR primers for the chloroplast genomes of higher plants [J].

Heinze, Berthold .

PLANT METHODS, 2007, 3 (1)

[4]

Metabolite profiling of grape: Flavonols and anthocyanins [J].

Mattivi, Fulvio ;

Guzzon, Raffaele ;

Vrhovsek, Urska ;

Stefanini, Marco ;

Velasco, Riccardo .

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 2006, 54 (20) :7692-7702

[5]

Quantitation of adenovirus DNA and virus particles with the PicoGreen fluorescent dye [J].

Murakami, P ;

McCaman, MT .

ANALYTICAL BIOCHEMISTRY, 1999, 274 (02) :283-288

[6]

Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.) [J].

Noir, S ;

Patheyron, S ;

Combes, MC ;

Lashermes, P ;

Chalhoub, B .

THEORETICAL AND APPLIED GENETICS, 2004, 109 (01) :225-230

[7]

Peterson D. G., 2000, Journal of Agricultural Genomics, V5, P1

[8]

Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), a plant containing high levels of polyphenolic compounds [J].

Peterson, DG ;

Boehm, KS ;

Stack, SM .

PLANT MOLECULAR BIOLOGY REPORTER, 1997, 15 (02) :148-153

[9]

DNA CONTENT OF BETA-VULGARIS CHLOROPLASTS DURING LEAF CELL EXPANSION [J].

TYMMS, MJ ;

SCOTT, NS ;

POSSINGHAM, JV .

PLANT PHYSIOLOGY, 1983, 71 (04) :785-788

[10]

Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir:: Problems and solutions [J].

Zharkikh, Andrey ;

Troggio, Michela ;

Pruss, Dmitry ;

Cestaro, Alessandro ;

Eldrdge, Glenn ;

Pindo, Massimo ;

Mitchell, Jeff T. ;

Vezzulli, Silvia ;

Bhatnagar, Satish ;

Fontana, Paolo ;

Viola, Roberto ;

Gutin, Alexander ;

Salamini, Francesco ;

Skolnick, Mark ;

Velasco, Riccardo .

JOURNAL OF BIOTECHNOLOGY, 2008, 136 (1-2) :38-43

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